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Merge pull request #1163 from IAlibay/patch-1
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Fixing some packmol interface docs.
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mattwthompson authored Feb 13, 2025
2 parents 6426579 + e8b00c6 commit 447743c
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions openff/interchange/components/_packmol.py
Original file line number Diff line number Diff line change
Expand Up @@ -596,7 +596,7 @@ def pack_box(
userguide/theory/05_other_features.html#periodic-boundary-conditions>`_.
target_density : openff.units.Quantity, optional
Target mass density for final system with units compatible with g / mL.
If ``None``, ``box_size`` must be provided.
If ``None``, ``box_vectors`` must be provided.
box_shape: Arraylike, optional
The shape of the simulation box, used in conjunction with
the ``target_density`` parameter. Should be a dimensionless array with
Expand Down Expand Up @@ -631,7 +631,7 @@ def pack_box(
Notes
-----
Returned topologies may have smaller or larger box vectors than what would be defined by the
target density if the box size is determined by `target_density`. When calling Packmol, each
target density if the box vectors are determined by `target_density`. When calling Packmol, each
linear dimension of the box is scaled up by 10%. However, Packmol by default adds a small
buffer (defined by the `tolerance` argument which otherwise defines the minimum distance,
default 2 Angstrom) at the end of the packed box, which causes small voids when tiling copies of
Expand Down Expand Up @@ -660,15 +660,15 @@ def pack_box(
target_density,
)

# Estimate the box_size from mass density if one is not provided.
# Estimate the box_vectors from mass density if one is not provided.
if target_density is not None:
box_vectors = _box_from_density(
molecules,
number_of_copies,
target_density,
box_shape,
)
# If neither box size nor density are given, take box vectors from solute
# If neither box vectors nor density are given, take box vectors from solute
# topology
if box_vectors is None:
box_vectors = solute.box_vectors # type: ignore[union-attr]
Expand Down Expand Up @@ -927,7 +927,7 @@ def solvate_topology_nonwater(
tolerance: Quantity = Quantity(2.0, "angstrom"),
) -> Topology:
"""
Add water and ions to neutralise and solvate a topology.
Solvate a topology with an arbitrary solvent.
Parameters
----------
Expand Down

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